Prediction with limited advice and multiarmed bandits with paid observations

We study two problems of online learning under restricted information access. In the first problem, prediction with limited advice, we consider a game of prediction with expert advice, where on each round of the game we query the advice of a subset of M out of N experts. We present an algorithm that achieves O(√(N/M)TlnN ) regret on T rounds of this game. The second problem, the multiarmed bandit with paid observations, is a variant of the adversarial N-armed bandit game, where on round t of the game we can observe the reward of any number of arms, but each observation has a cost c. We present an algorithm that achieves O((cNlnN) 1/3 T2/3+√TlnN ) regret on T rounds of this game in the worst case. Furthermore, we present a number of refinements that treat arm- and time-dependent observation costs and achieve lower regret under benign conditions. We present lower bounds that show that, apart from the logarithmic factors, the worst-case regret bounds cannot be improved.

Contemporary public spaces in urban knowledge precincts : observations from Brisbane, Australia

The advanced era of knowledge-based urban development has led to an unprecedented increase in mobility of people and the subsequent growth in the new typology of agglomerated enclaves of knowledge such as urban knowledge precincts. A new role has been assigned to contemporary public spaces of these precincts to attract and retain the mobile knowledge workforce for long by creating a sense of place for them. This paper sheds light over the place making in the globalised knowledge economy world which develops a sense of permanence spatio-temporally to knowledge workers displaying a set of particular characteristics and simultaneously is process-dependent getting developed by the internal and external flows and contributing substantially in the development of the broader context it stands in relation with. The paper highlights the observations from Australia’s new world city Brisbane to outline the application of urban design as a tool to create and sustain this bipartite place making in urban knowledge precincts, which caters diverse range of social, cultural and democratic needs. It seeks to analyse the modified permeable typology of public spaces that makes it more viable and adaptive as per the changing needs of the contemporary globalised or in other words knowledge society. This research has taken an overall process-based approach reflecting how urban design is an assemblage of the encompassing processes that underlay the resultant place making. It explores how the permeable design typology of these contemporary precincts in Brisbane develops a progressive sense of place that makes them stimulating, effervescent and vibrant.

Species differences in acrylonitrile metabolism and toxicity between experimental animals and humans based on observations in human accidental poisonings

The high acute toxicity of acrylonitrile may be a result of its intrinsic biological reactivity or of its metabolite cyanide. Intravenous N-acetylcysteine has been recommended for treatment of accidental intoxications in acrylonitrile workers, but such recommendations vary internationally. Acrylonitrile is metabolized in humans and experimental animals via two competing pathways; the glutathione-dependent pathway is considered to represent an avenue of detoxication whilst the oxidative pathway leads to a genotoxic epoxide, cyanoethylene oxide, and to elimination of cyanide. Cases of acute acrylonitrile overexposure or intoxication have occurred within persons having industrial contact with acrylonitrile; the route of exposure was by inhalation and/or by skin contact. The combined observations lead to the conclusion of a much higher impact of the oxidative metabolism of acrylonitrile in humans than in rodents. This is confirmed by differences in the clinical picture of acute life-threatening intoxications in both species, as well as by differential efficacies of antidotes. A combination of N-acetylcysteine with sodium thiosulfate seems an appropriate measure for antidote therapy of acute acrylonitrile intoxications. Clinical observations also highlight the practical importance of human individual susceptibility differences. Furthermore, differential adduct monitoring, assessing protein adducts with different rates of decay, enables the development of more elaborated biological monitoring strategies for the surveillance of workers with potential acrylonitrile contact.

Growth curves with time-dependent explanatory variables

A class of growth models incorporating time-dependent factors and stochastic perturbations are introduced. The proposed model includes the existing growth models used in fisheries as special cases. Particular attention is given to growth of a population (in average weight or length) from which observations are taken randomly each time and the analysis of tag-recapture data. Two real data sets are used for illustration: (a) to estimate the seasonal effect and population density effect on growth of farmed prawn (Penaeus monodon) from weight data and (b) to assess the effect of tagging on growth of barramundi (Lates calcarifer)

Molecular mechanisms of bacteriophage phi6 RNA-dependent RNA polymerase and its utilization in biotechnology

Double-stranded RNA (dsRNA) viruses encode only a single protein species that contains RNA-dependent RNA polymerase (RdRP) motifs. This protein is a central component in the life cycle of a dsRNA virus, carrying out both RNA transcription and replication. The architecture of viral RdRPs resembles that of a 'cupped right hand' with fingers, palm and thumb domains. Those applying de novo initiation have additional structural features, including a flexible C-terminal domain that constitutes the priming platform. Moreover, viral RdRPs must be able to interact with the incoming 3'-terminus of the template and position it so that a productive binary complex is formed. Bacteriophage phi6 of the Cystoviridae family is to date one of the best studied dsRNA viruses. The purified recombinant phi6 RdRP is highly active in vitro and possesses both RNA replication and transcription activities. The extensive biochemical observations and the atomic level crystal structure of the phi6 RdRP provides an excellent platform for in-depth studies of RNA replication in vitro. In this thesis, targeted structure-based mutagenesis, enzymatic assays and molecular mapping of phi6 RdRP and its RNA were used to elucidate the formation of productive RNA-polymerase binary complexes. The positively charged rim of the template tunnel was shown to have a significant role in the engagement of highly structured ssRNA molecules, whereas specific interactions further down in the template tunnel promote ssRNA entry to the catalytic site. This work demonstrated that by aiding the formation of a stable binary complex with optimized RNA templates, the overall polymerization activity of the phi6 RdRP can be greatly enhanced. Furthermore, proteolyzed phi6 RdRPs that possess a nick in the polypeptide chain at the hinge region, which is part of the extended loop, were better suited for catalysis at higher temperatures whilst favouring back-primed initiation. The clipped C-terminus remains associated with the main body of the polymerase and the hinge region, although structurally disordered, is involved in the control of C-terminal domain displacement. The accumulated knowhow on bacteriophage phi6 was utilized in the development of two technologies for the production of dsRNA: (i) an in vitro system that combines the T7 RNA polymerase and the phi6 RdRP to generate dsRNA molecules of practically unlimited length, and (ii) an in vivo RNA replication system based on restricted infection with phi6 polymerase complexes in bacterial cells to produce virtually unlimited amounts of dsRNA. The pools of small interfering RNAs derived from dsRNA produced by these systems were validated and shown to efficiently decrease the expression of both exogenous and endogenous targets.

Serine Hydroxymethyltransferase from Mung Bean (Vigna radiata) Is Not a Pyridoxal-5'-Phosphate- Dependent Enzyme

Serine hydroxymethyltransferase from mammalian and bacterial sources is a pyridoxal-5'-phosphate-containing enzyme, but the requirement of pyridoxal-5'-phosphate for the activity of the enzyme from plant sources is not clear. The specific activity of serine hydroxymethyltransferase isolated from mung bean (Vigna radiata) seedlings in the presence and absence of pyridoxal-5'-phosphate was comparable at every step of the purification procedure. The mung bean enzyme did not show the characteristic visible absorbance spectrum of pyridoxal-5'-phosphate protein. Unlike the enzymes from sheep, monkey, and human liver, which were converted to the apoenzyme upon treatment with L-cysteine and dialysis, the mung bean enzyme similarly treated was fully active. Additional evidence in support of the suggestion that pyridoxal-5'-phosphate may not be required for the mung bean enzyme was the observation that pencillamine, a well-known inhibitor of pyridoxal-5'-phosphate enzymes, did not perturb the enzyme spectrum or inhibit the activity of mung bean serine hydroxymethyltransferase. The sheep liver enzyme upon interaction with O-amino-D-serine gave a fluorescence spectrum with an emission maximum at 455 nm when excited at 360 nm. A 100-fold higher concentration of mung bean enzyme-O-amino-D-serine complex did not yield a fluorescence spectrum. The following observations suggest that pyridoxal-5'-phosphate normally present as a coenzyme in serine hydroxymethyltransferase was probably replaced in mung bean serine hydroxymethyltransferase by a covalently bound carbonyl group: (a) inhibiton by phenylhydrazine and hydroxylamine, which could not be reversed by dialysis and or addition of pyridoxal-5'-phosphate; (b) irreversible inactivation by sodium borohydride; (c) a spectrum characteristic of a phenylhydrazone upon interaction with phenylhydrazine; and (d) the covalent labeling of the enzyme with substrate/product serine and glycine upon reduction with sodium borohydride. These results indicate that in mung bean serine hydroxymethyltransferase, a covalently bound carbonyl group has probably replaced the pyridoxal-5'-phosphate that is present in the mammalian and bacterial enzymes.

Size dependent microstructure for Ag-Ni nanoparticles

The Ag-Ni system is characterized by large differences in atomic sizes (14%) and a positive heat of mixing (+23 kJ mol(-1)). The binary equilibrium diagram for this system therefore exhibits a large miscibility gap in both solid and liquid state. This paper explores the size-dependent changes in microstructure and the suppression of the miscibility gap which occurs when free alloy particles of nanometer size are synthesized by co-reduction of Ag and Ni metal precursors. The paper reports that complete mixing between Ag and Ni atoms could be achieved for smaller nanoparticles (<7 nm). These particles exhibit a single-phase solid solution with face-centered cubic (fcc) structure. With increase in size, the nanoparticles revealed two distinct regions. One of the regions is composed of pure Ag. This region partially surrounds a region of fcc solid solution at an early stage of decomposition. Experimental observations were compared with the results obtained from the thermodynamic calculations, which compared the free energies corresponding to a physical mixture of pure Ag and Ni phases and a fcc Ag-Ni solid solution for different particle sizes. Results from the theoretical calculations revealed that, for the Ag-Ni system, solid solution was energetically preferred over the physical mixture configuration for particle sizes of 7 nm and below. The experimentally observed two-phase microstructure for larger particles was thus primarily due to the growth of Ag-rich regions epitaxially on initially formed small fcc Ag-Ni nanoparticles. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Synthesis dependent characteristics of Sr1-xMnxTiO3 (x=0.03, 0.05, 0.07 and 0.09)

Sr1-xMnxTiO3 (where x=0.03, 0.05, 0.07 and 0.09) was synthesized via different routes that include solid-state, oxalate precipitation and freeze drying. In oxalate precipitation technique, compositions corresponding to 3 and 5 mol% doping of Mn were monophasic whereas the higher compositions revealed the presence of the secondary phases such as MnO, Mn3O4 etc., as confirmed by high resolution X-ray diffraction (XRD) studies. The decomposition behavior of the precursors prepared using oxalate precipitation method corresponding to the above mentioned compositions was studied. Nanopowders of compositions pertaining to 5 to 9 mol% of Mn doping were obtained using freeze-drying technique. The average crystallite size of these nanopowders was found to be in the 35 to 65 nm range. The microstructural studies carried out on the sintered ceramics, fabricated using powders synthesized by different routes established the fine grained nature ( < 1 mu m) of the one obtained by freeze drying method. Raman scattering studies were carried out in order to complement the observations made from XRD regarding the phase purity. The dielectric properties of the ceramics obtained by different synthesis routes were studied in the 80-300 K temperature range at 100 kHz and the effect of grain size has been discussed. (C) 2012 Elsevier Inc. All rights reserved.

Size dependent structural relaxations and dielectric properties induced by surface functionalized MWNTs in poly(vinylidene fluoride)/poly(methyl methacrylate) blends

Structural dynamics, dielectric permittivity and ferroelectric properties in poly(vinylidene fluoride) (PVDF)/poly(methyl methacrylate) (PMMA) (PVDF/PMMA) blends with respect to crystalline morphology was systematically investigated in presence of amine functionalized MWNTs (NH2-MWNTs) using dielectric spectroscopy. The crystalline morphology and the crystallization driven demixing in the blends was assessed by light microscopy (LM), wide angle X-ray diffraction (WXRD) and, in situ, by shear rheology. The crystal nucleation activity of PVDF was greatly induced by NH2-MWNTs, which also showed two distinct structural relaxations in dielectric loss owing to mobility confinement of PVDF chains and smaller cooperative lengths. The presence of crystal-amorphous interphase was supported by the presence of interfacial polarization at lower frequencies in the dielectric loss spectra. On contrary, the control blends showed a single broad relaxation at higher frequency due to defective crystal nuclei. This was further supported by monitoring the dielectric relaxations during isothermal crystallization of PVDF in the blends. These observations were addressed with respect to the spherulite sizes which were observed to be larger in case of blends with NH2-MWNTs. Higher dielectric permittivity with minimal losses was also observed in blends with NH2-MWNTs as compared to neat PVDF. Polarization obtained using P-E (polarization-electric field) hysteresis loops was higher in case of blends with NH2-MWNTs in contrast to control blends and PVDF. These observations were corroborated with the charge trapped at the crystal-amorphous interphase and larger crystal sizes in the blends with NH2-MWNTs. The microstructure and localization of MWNTs were assessed using SEM.

RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Synthesis and Mechanism of Composition and Size Dependent Morphology Selection in Nanoparticles of Ag-Cu Alloys Processed by Laser Ablation Under Liquid Medium

We have synthesized Ag-Cu alloy nanoparticles of four different compositions by using the laser ablation technique with the target under aqueous medium. Following this, we report a morphological transition in the nanoparticles from a normal two-phase microstructure to a structure with random segregation and finally a core shell structure at small sizes as a function of Cu concentration. To illustrate the composition dependence of morphology, we report observations carried out on nanoparticles of two different sizes: similar to 5 and similar to 20 nm. The results could be rationalized through the thermodynamic modeling of free energy of phase mixing and wettability of the alloying phases.

Magnetic skin layer of NiO(100) probed by polarization-dependent spectromicroscopy

Using polarization-dependent x-ray photoemission electron microscopy, we have investigated the surface effects on antiferromagnetic (AFM) domain formation. Depth-resolved information obtained from our study indicates the presence of strain-induced surface AFM domains on some of the cleaved NiO(100) crystals, which are unusually thinner than bulk AFM domain wall widths (similar to 150 nm). Existence of such magnetic skin layer is substantiated by exchange-coupled ferromagnetic Fe domains in Fe/NiO(100), thereby evidencing the influence of this surface AFM domains on interfacial magnetic coupling. Our observations demonstrate a depth evolution of AFM structure in presence of induced surface strain, while the surface symmetry-breaking in absence of induced strain does not modify the bulk AFM domain structure. Realization of such thin surface AFM layer will provide better microscopic understanding of the exchange bias phenomena. (C) 2014 AIP Publishing LLC.

Depression biased non-Hebbian spike-timing-dependent synaptic plasticity in the rat subiculum

The subiculum is a structure that forms a bridge between the hippocampus and the entorhinal cortex (EC), and plays a major role in the memory consolidation process. Here, we demonstrate spike-timing-dependent plasticity (STDP) at the proximal excitatory inputs on the subicular pyramidal neurons of juvenile rat. Causal (positive) pairing of a single EPSP with a single back-propagating action potential (bAP) after a time interval of 10 ms (+10 ms) failed to induce plasticity. However, increasing the number of bAPs in a burst to three, at two different frequencies of 50 Hz (bAP burst) and 150 Hz, induced long-term depression (LTD) after a time interval of +10 ms in both the regular-firing (RF), and the weak burst firing (WBF) neurons. The LTD amplitude decreased with increasing time interval between the EPSP and the bAP burst. Reversing the order of the pairing of the EPSP and the bAP burst induced LTP at a time interval of -10 ms. This finding is in contrast with reports at other synapses, wherein prebefore postsynaptic (causal) pairing induced LTP and vice versa. Our results reaffirm the earlier observations that the relative timing of the pre- and postsynaptic activities can lead to multiple types of plasticity profiles. The induction of timing-dependent LTD (t-LTD) was dependent on postsynaptic calcium change via NMDA receptors in the WBF neurons, while it was independent of postsynaptic calcium change, but required active L-type calcium channels in the RF neurons. Thus the mechanism of synaptic plasticity may vary within a hippocampal subfield depending on the postsynaptic neuron involved. This study also reports a novel mechanism of LTD induction, where L-type calcium channels are involved in a presynaptically induced synaptic plasticity. The findings may have strong implications in the memory consolidation process owing to the central role of the subiculum and LTD in this process.

Brain type II calcium and calmodulin-dependent protein kinase: characterization of a brain-region specific isozyme and regulation by autophosphorylation

A variety of molecular approaches have been used to investigate the structural and enzymatic properties of rat brain type ll Ca^(2+) and calmodulin-dependent protein kinase (type ll CaM kinase). This thesis describes the isolation and biochemical characterization of a brain-region specific isozyme of the kinase and also the regulation the kinase activity by autophosphorylation.

The cerebellar isozyme of the type ll CaM kinase was purified and its biochemical properties were compared to the forebrain isozyme. The cerebellar isozyme is a large (500-kDa) multimeric enzyme composed of multiple copies of 50-kDa α subunits and 60/58-kDa β/β’ subunits. The holoenzyme contains approximately 2 α subunits and 8 β subunits. This contrasts to the forebrain isozyme, which is also composed of and β/β'subunits, but they are assembled into a holoenzyme of approximately 9 α subunits and 3 β/β ' subunits. The biochemical and enzymatic properties of the two isozymes are similar. The two isozymes differ in their association with subcellular structures. Approximately 85% of the cerebellar isozyme, but only 50% of the forebrain isozyme, remains associated with the particulate fraction after homogenization under standard conditions. Postsynaptic densities purified from forebrain contain the forebrain isozyme, and the kinase subunits make up about 16% of their total protein. Postsynaptic densities purified from cerebellum contain the cerebellar isozyme, but the kinase subunits make up only 1-2% of their total protein.

The enzymatic activity of both isozymes of the type II CaM kinase is regulated by autophosphorylation in a complex manner. The kinase is initially completely dependent on Ca^(2+)/calmodulin for phosphorylation of exogenous substrates as well as for autophosphorylation. Kinase activity becomes partially Ca^(2+) independent after autophosphorylation in the presence of Ca^(2+)/calmodulin. Phosphorylation of only a few subunits in the dodecameric holoenzyme is sufficient to cause this change, suggesting an allosteric interaction between subunits. At the same time, autophosphorylation itself becomes independent of Ca^(2+) These observations suggest that the kinase may be able to exist in at least two stable states, which differ in their requirements for Ca^(2+)/calmodulin.

The autophosphorylation sites that are involved in the regulation of kinase activity have been identified within the primary structure of the α and β subunits. We used the method of reverse phase-HPLC tryptic phosphopeptide mapping to isolate individual phosphorylation sites. The phosphopeptides were then sequenced by gas phase microsequencing. Phosphorylation of a single homologous threonine residue in the α and β subunits is correlated with the production of the Ca^(2+) -independent activity state of the kinase. In addition we have identified several sites that are phosphorylated only during autophosphorylation in the absence of Ca^(2+)/ calmodulin.

The instability of fluids with time dependent heating

The stability of a fluid having a non-uniform temperature stratification is examined analytically for the response of infinitesimal disturbances. The growth rates of disturbances have been established for a semi-infinite fluid for Rayleigh numbers of 10³, 10⁴, and 10⁵ and for Prandtl numbers of 7.0 and 0.7.

The critical Rayleigh number for a semi-infinite fluid, based on the effective fluid depth, is found to be 32, while it is shown that for a finite fluid layer the critical Rayleigh number depends on the rate of heating. The minimum critical Rayleigh number, based on the depth of a fluid layer, is found to be 1340.

The stability of a finite fluid layer is examined for two special forms of heating. The first is constant flux heating, while in the second, the temperature of the lower surface is increased uniformly in time. In both cases, it is shown that for moderate rates of heating the critical Rayleigh number is reduced, over the value for very slow heating, while for very rapid heating the critical Rayleigh number is greatly increased. These results agree with published experimental observations.

The question of steady, non-cellular convection is given qualitative consideration. It is concluded that, although the motion may originate from infinitesimal disturbances during non-uniform heating, the final flow field is intrinsically non-linear.